Machine Learning Research Engineer

Machine Learning Research EngineerEmeryville, California, United States; Hybrid (2-3 days on-site)Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in 2022 and headquartered in Emeryville, CA, Profluent is backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures and has raised over $150M to date.We're looking for an experienced Machine Learning Engineer to build and improve the models and ML systems that drive our protein design efforts. In this role, you'll deploy and optimize large-scale generative models for protein design, and develop the surrounding infrastructure and tooling that enable our ML and protein design scientists to work faster and more confidently. As an early member of a small, fast-moving engineering team, you'll have significant ownership over our ML stack and the opportunity to shape how our platform evolves.ResponsibilitiesBuild robust, reproducible and user-friendly pipelines for automated model fine-tuning, alignment and evaluationDesign and implement modular, easy-to-maintain, multi-model pipelines for protein designDevelop highly scalable ETL pipelines to process petabyte-scale protein data for model pretrainingOptimize model training and inference code to maximize throughput and resource utilization when deployed at scaleDevelop software and infrastructure that enable the ML team to work quickly and frictionlessly in distributed and multi-cloud environmentsPartner with ML and protein design scientists to prototype research ideas and bring them into productionWho You AreYou're comfortable taking ownership and working independently in a fast-moving environmentYou're an execution-oriented engineer who maintains high standards, and focuses on the highest-impact workYou're comfortable owning the full stack of your work, from training code to the infrastructure it runs onYou care deeply about model quality, efficiency, and reliabilityYou're willing to step beyond your core responsibilities when the team needs itRepresentative ProjectsBuilding hyperparameter search frameworks for SFT and Alignment workflowsIncreasing protein language model throughput during long context generationUpdating existing model architectures to work and run efficiently on new GPU hardwareImplementing a protein design pipeline that integrates prompt retrieval, sequence generation, attribute prediction, and structure predictionEstablishing an ETL pipeline for sampling and tokenizing training datasets from an internal database of billions of sequencesDeveloping a benchmarking and evaluation system for newly trained sequence generation modelsContributing to the development of an internal service that provides transparent multi-node job submission for ML scientistsQualificationsBS or MS in Computer Science, Machine Learning, or a related field3+ years of hands-on experience building and training ML models in PyTorchStrong Python and software engineering fundamentals, including testing, code quality, and version controlExperience profiling, benchmarking, and optimizing ML model training and inferenceExperience implementing or optimizing transformer-based architecturesFamiliarity with cloud infrastructure and containerization (GCP, AWS, Azure, Kubernetes, Docker)Strong fundamentals in ML, statistics, and/or linear algebraPreferencesFamiliarity with protein language models or computational biologyExperience with GPU-level optimization (CUDA, Triton)Experience with distributed training (DDP, FSDP, multi-node GPU clusters)Experience with databases and data processing pipelinesExperience orchestrating multi-step ML workflowsExperience building backend systems that serve ML models in productionContributions to open source ML projects or published researchWhat We OfferHigh-growth opportunity with meaningful impact on the future of protein designCompetitive compensation package with equity participation401(k) with a strong employer matchComprehensive benefits including health/dental/vision insuranceGenerous PTO policy and commitment to work-life balanceProfessional development opportunities in a cutting-edge field at the intersection of AI and biologyProfluent Bio, Inc is an equal opportunity employer promoting diversity and inclusion in the workspace. We do not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical conditions, veteran status, sexual orientation, gender (including gender identity and gender expression), sex (which includes pregnancy, childbirth, and breastfeeding), genetic information, taking or requesting statutorily protected leave, or any other basis protected by law.Legal authorization to work in the United States is required. In compliance with federal law, all persons hired must verify their identity and work eligibility and complete the required employment verification form upon hire.Hiring Salary Range$200,000 - $330,000 USD